Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA.

Ligands that stabilize non-canonical DNA structures called G-quadruplexes (GQs) might have applications in medicine as anti-cancer agents, due to the involvement of GQ DNA in a variety of cancer-related biological processes. Five derivatives of 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4), where a N-methylpyridyl group was replaced with phenyl (4P3), 4-aminophenyl (PN3M), 4-phenylamidoproline (PL3M), or 4-carboxyphenyl (PC3M and P2C2M) were investigated for their interactions with human telomeric DNA (Tel22) using fluorescence resonance energy transfer (FRET) assay, and UV-visible and circular dichroism spectroscopies in K+ buffer. The molecules are cationic or zwitterionic with an overall charge of 3+ (4P3, PN3M, and PL3M), 2+ (PC3M) or neutral (P2C2M). All porphyrins except P2C2M stabilize human telomeric DNA in FRET assays by ∼20 °C at 5 eq CD melting experiments suggest that 4P3 is the most stabilizing ligand with a stabilization temperature of 16.8 °C at 4 eq. Importantly, 4P3, PC3M and PL3M demonstrate excellent selectivity for quadruplexes, far superior to that of TMPyP4. Binding constants, determined using UV-vis titrations, correlate with charge: triply cationic 4P3, PN3M and PL3M display Ka of 5-9 µM-1, doubly cationic PC3M displays Ka of 1 µM-1, and neutral P2C2M displays weak-to-no binding. UV-vis data suggest that binding interactions are driven by electrostatic attractions and that the binding mode may be base-stacking (or end-stacking) judging by the high values of red shift (15-20 nm) and hypochromicity (40-50%). We conclude that lowering the charge on TMPyP4 to 3+ can achieve the desired balance between stabilizing ability, affinity, and high selectivity required for an excellent quadruplex ligand.